How to create a runnable jar file from multiple java packages. The below example has two packages mypkg1 & mypkg2 with the below directory structure
As you can see below I have 3 java files and two packages

# pwd 
/tmp/prog

# du -a
4       ./mypkg1/One.java
4       ./mypkg1/Two.java
16      ./mypkg1
4       ./mypkg2/Res.java
8       ./mypkg2

Example java main method file.

package mypkg1;

import mypkg2.Res;

public class One
{
        public static void main(String[] args) {
                Two two = new Two();
                Res res = new Res();
                System.out.println(two.Two(2, 2));
                System.out.println(res.Res(4, 2));
        }
}

Create a Manifest file Note: mypkg1 contains the main and One is the class called

cat mypkg1/manifest.txt
Main-Class: mypkg1.One

Note: Make sure to leave two empty lines at the end
Lets first compile to java byte-code.

javac mypkg*/*.java

Now we are ready to compile / create the jar file.

jar -cvfm mypkg1.jar mypkg1/mainfest.txt mypkg*/*.class
added manifest
adding: mypkg1/One.class(in = 510) (out= 354)(deflated 30%)
adding: mypkg1/Two.class(in = 249) (out= 199)(deflated 20%)
adding: mypkg2/Res.class(in = 249) (out= 199)(deflated 20%)

To use the jar file just run

java -jar mypkg1.jar

One last word about extra library files or any other static data. By default java will search library and shared objects (so) files under the project folder/lib, make sure to include that in the jar file if needed. alternatively use Apache Ant to auto build your project